Genome rearrangements have been implicated as a driving mechanism in the speciation of many organisms, as well as in the progression of cancers and various human aneuploidy syndromes. Using microarray-based Comparative Genomic Hybridization (array-CGH), we will track, on a whole-genome scale, the chromosomal rearrangements that occur during each step of de novo speciation in hybrid yeasts formed between Saccharomyces cerevisiae and each of the 4 other sequenced Saccharomyces species. We will design a set of four novel oligomer microarrays, such that each microarray design will contain probes for S. cerevisiae, and probes for one of the other four sensu stricto species; these arrays will be tailored specifically to detect chromosomal rearrangements-such as aneuploidy, translocations, amplifications and deletions-- that occur in either parental genome during the process of hybrid speciation. We will also use these arrays to similarly investigate whether the nascent hybrid yeast species, when grown in chemostats under differing conditions, exhibit characteristic sets of genome rearrangements that can be correlated with specific environmental pressures, and to determine the stability of these genome rearrangements during long-term growth. These studies will represent the first genome-wide assessment of the extent and types of genome rearrangements that occur during real-time speciation and adaptation. They will enable us to elucidate not only potential mechanisms of genome rearrangement, but also potential mechanisms of speciation. By establishing whether specific large-scale genome rearrangements are associated with specific selective pressures, we will gain insight into the role that genome plasticity plays in adaptive evolution. Achievement of these aims is expected to shed new light on the importance of genome rearrangements in driving adaptation and speciation, as well in cancer progression and human aneuploidy syndromes.